Exploratory data analysis of physicochemical parameters of natural antimicrobial and anticancer peptides: Unraveling the patterns and trends for the rational design of novel peptides
Introduction: Peptide-based research has attained new avenues in the antibiotics and cancer drug resistance era. The basis of peptide design research lies in playing with or altering physicochemical parameters. Here in this work, we have done exploratory data analysis (EDA) of physicochemical parame...
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| Format: | Article |
| Language: | English |
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Tabriz University of Medical Sciences
2024-01-01
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| Series: | BioImpacts |
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| Online Access: | https://bi.tbzmed.ac.ir/PDF/bi-14-26438.pdf |
| _version_ | 1797323306059169792 |
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| author | Sandeep Saini Aayushi Rathore Sheetal Sharma Avneet Saini |
| author_facet | Sandeep Saini Aayushi Rathore Sheetal Sharma Avneet Saini |
| author_sort | Sandeep Saini |
| collection | DOAJ |
| description | Introduction: Peptide-based research has attained new avenues in the antibiotics and cancer drug resistance era. The basis of peptide design research lies in playing with or altering physicochemical parameters. Here in this work, we have done exploratory data analysis (EDA) of physicochemical parameters of antimicrobial peptides (AMPs) and anticancer peptides (ACPs), two promising therapeutics for microbial and cancer drug resistance to deduce patterns and trends. Methods: Briefly, we have captured the natural AMPs and ACPs data from the APD3 database. After cleaning the data manually and by CD-HIT web server, further data analysis has been done using Python-based packages, modlAMP and Pandas. We have extracted the descriptive statistics of 10 physicochemical parameters of AMPs and ACPs to build a comprehensive dataset containing all major parameters. The global analysis of datasets has been done using modlAMP to find the initial patterns in global data. The subsets of AMPs and ACPs were curated based on the length of the peptides and were analyzed by Pandas package to deduce the graphical profile of AMPs and ACPs. Results: EDA of AMPs and ACPs shows selectivity in the length and amino acid compositions. The distribution of physicochemical parameters in defined quartile ranges was observed in the descriptive statistical and graphical analysis. The preferred length range of AMPs and ACPs was found to be 21-30 amino acids, whereas few outliers in each parameter were evident after EDA analysis. Conclusion: The derived patterns from natural AMPs and ACPs can be used for the rational design of novel peptides. The statistical and graphical data distribution findings will help in combining the different parameters for potent design of novel AMPs and ACPs. |
| first_indexed | 2024-03-08T05:26:50Z |
| format | Article |
| id | doaj.art-344fe4cab199459c93b7ba4541fde9cb |
| institution | Directory Open Access Journal |
| issn | 2228-5652 2228-5660 |
| language | English |
| last_indexed | 2024-03-08T05:26:50Z |
| publishDate | 2024-01-01 |
| publisher | Tabriz University of Medical Sciences |
| record_format | Article |
| series | BioImpacts |
| spelling | doaj.art-344fe4cab199459c93b7ba4541fde9cb2024-02-06T10:15:16ZengTabriz University of Medical SciencesBioImpacts2228-56522228-56602024-01-01141264382643810.34172/bi.2023.26438bi-26438Exploratory data analysis of physicochemical parameters of natural antimicrobial and anticancer peptides: Unraveling the patterns and trends for the rational design of novel peptidesSandeep Saini0Aayushi Rathore1Sheetal Sharma2Avneet Saini3Department of Biophysics, Panjab University, Sector 25, Chandigarh 160014, IndiaInstitute of Bioinformatics and Applied Biotechnology, Biotech Park, Bengaluru 560100, IndiaDepartment of Biophysics, Panjab University, Sector 25, Chandigarh 160014, IndiaDepartment of Biophysics, Panjab University, Sector 25, Chandigarh 160014, IndiaIntroduction: Peptide-based research has attained new avenues in the antibiotics and cancer drug resistance era. The basis of peptide design research lies in playing with or altering physicochemical parameters. Here in this work, we have done exploratory data analysis (EDA) of physicochemical parameters of antimicrobial peptides (AMPs) and anticancer peptides (ACPs), two promising therapeutics for microbial and cancer drug resistance to deduce patterns and trends. Methods: Briefly, we have captured the natural AMPs and ACPs data from the APD3 database. After cleaning the data manually and by CD-HIT web server, further data analysis has been done using Python-based packages, modlAMP and Pandas. We have extracted the descriptive statistics of 10 physicochemical parameters of AMPs and ACPs to build a comprehensive dataset containing all major parameters. The global analysis of datasets has been done using modlAMP to find the initial patterns in global data. The subsets of AMPs and ACPs were curated based on the length of the peptides and were analyzed by Pandas package to deduce the graphical profile of AMPs and ACPs. Results: EDA of AMPs and ACPs shows selectivity in the length and amino acid compositions. The distribution of physicochemical parameters in defined quartile ranges was observed in the descriptive statistical and graphical analysis. The preferred length range of AMPs and ACPs was found to be 21-30 amino acids, whereas few outliers in each parameter were evident after EDA analysis. Conclusion: The derived patterns from natural AMPs and ACPs can be used for the rational design of novel peptides. The statistical and graphical data distribution findings will help in combining the different parameters for potent design of novel AMPs and ACPs.https://bi.tbzmed.ac.ir/PDF/bi-14-26438.pdfantimicrobial peptideanticancer peptidedata analysisrational designpeptide propertiespatterns and trends |
| spellingShingle | Sandeep Saini Aayushi Rathore Sheetal Sharma Avneet Saini Exploratory data analysis of physicochemical parameters of natural antimicrobial and anticancer peptides: Unraveling the patterns and trends for the rational design of novel peptides BioImpacts antimicrobial peptide anticancer peptide data analysis rational design peptide properties patterns and trends |
| title | Exploratory data analysis of physicochemical parameters of natural antimicrobial and anticancer peptides: Unraveling the patterns and trends for the rational design of novel peptides |
| title_full | Exploratory data analysis of physicochemical parameters of natural antimicrobial and anticancer peptides: Unraveling the patterns and trends for the rational design of novel peptides |
| title_fullStr | Exploratory data analysis of physicochemical parameters of natural antimicrobial and anticancer peptides: Unraveling the patterns and trends for the rational design of novel peptides |
| title_full_unstemmed | Exploratory data analysis of physicochemical parameters of natural antimicrobial and anticancer peptides: Unraveling the patterns and trends for the rational design of novel peptides |
| title_short | Exploratory data analysis of physicochemical parameters of natural antimicrobial and anticancer peptides: Unraveling the patterns and trends for the rational design of novel peptides |
| title_sort | exploratory data analysis of physicochemical parameters of natural antimicrobial and anticancer peptides unraveling the patterns and trends for the rational design of novel peptides |
| topic | antimicrobial peptide anticancer peptide data analysis rational design peptide properties patterns and trends |
| url | https://bi.tbzmed.ac.ir/PDF/bi-14-26438.pdf |
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